@@ -87,7 +87,12 @@ exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)

 export(genotypeSummary,

        shrinkSummary,

        estimateCnParameters,

-       shrinkGenotypeSummaries, indexComplete, summarizeSnps, constructIlluminaAssayData, crlmmIlluminaV2, ACN, C1, C2, C3, fit.lm3)

+       shrinkGenotypeSummaries,

+##       indexComplete,

+       summarizeSnps,

+       constructIlluminaAssayData,

+       ACN, C1, C2, C3, fit.lm3,

+       linesCNSet)

 exportMethods(N.AA, N.AB, N.BB, "N.AA<-", "N.AB<-", "N.BB<-", medianA.AA, "medianA.AA<-")

@@ -43,7 +43,7 @@ setMethod("Ns", signature(object="AssayData"),

 		  return(res)

 	  })

 setMethod("corr", signature(object="AssayData"),

-	  function(object, i, j, ...){

+	  function(object, ...){

 		  dotArgs <- names(list(...))

 		  missing.i <- !("i" %in% dotArgs)

 		  missing.j <- !("j" %in% dotArgs)

@@ -410,7 +410,6 @@ ACN <- function(object, allele, i , j){

 		is.X <- chromosome(object)[i]==23 & is.ann

 		is.auto <- chromosome(object)[i] < 23 & is.ann

 		is.snp <- isSnp(object)[i] & is.ann

-

 	} else{

 		is.ann <- !is.na(chromosome(object))

 		is.X <- chromosome(object)==23 & is.ann

@@ -509,8 +508,8 @@ ACN <- function(object, allele, i , j){

 			acn.index <- which(!is.snp)

 			marker.index <- i[!is.snp]

 			acn[acn.index, ] <- 0

-		} else{

-			## SNPs

+		}

+		if(any(is.snp)){

 			if(any(is.auto)){

 				## autosomal SNPs

 				acn.index <- which(is.auto & is.snp)

@@ -6,21 +6,28 @@ setMethod("lines", signature=signature(x="CNSet"),

 linesCNSet <- function(x, y, batch, copynumber, x.axis="A", ...){

 	require(ellipse)

 	object <- x

-	I <- y

-	stopifnot(length(I) == 1)

-	column <- grep(batch, batchNames(object))

-	stopifnot(length(column) == 1)

-	nuA <- nu(object, "A")[I, column]

-	nuB <- nu(object, "B")[I, column]

-	phiA <- phi(object, "A")[I, column]

-	phiB <- phi(object, "B")[I, column]

-	tau2A <- tau2(object, "A")[I, column]

-	tau2B <- tau2(object, "B")[I, column]

-	sigma2A <- sigma2(object, "A")[I, column]

-	sigma2B <- sigma2(object, "B")[I, column]

-	corrAB <- corr(object, "AB")[I, column]

-	corrAA <- corr(object, "AA")[I, column]

-	corrBB <- corr(object, "BB")[I, column]

+	marker.index <- y

+	stopifnot(length(marker.index) == 1)

+	batch.index <- match(batch, batchNames(object))

+	stopifnot(length(batch.index) == 1)

+	nuA <- nu(object, "A")[marker.index, batch.index]

+	nuB <- nu(object, "B")[marker.index, batch.index]

+	phiA <- phi(object, "A")[marker.index, batch.index]

+	phiB <- phi(object, "B")[marker.index, batch.index]

+

+	taus <- tau2(object, i=marker.index, j=batch.index)

+	tau2A <- taus[, "A", "BB", ]

+	tau2B <- taus[, "B", "AA", ]

+	sigma2A <- taus[, "A", "AA", ]

+	sigma2B <- taus[, "B", "BB", ]

+##	tau2A <- tau2(object, "A")[marker.index, batch.index]

+##	tau2B <- tau2(object, "B")[marker.index, batch.index]

+##	sigma2A <- sigma2(object, "A")[marker.index, batch.index]

+##	sigma2B <- sigma2(object, "B")[marker.index, batch.index]

+	cors <- corr(object, i=marker.index, j=batch.index)[, , ]

+	corrAB <- cors[["AB"]]

+	corrAA <- cors[["AA"]]

+	corrBB <- cors[["BB"]]

 	if(all(is.na(nuA))) {

 		message("Parameter estimates for batch ", batch, " not available")

 		next()

@@ -47,7 +47,7 @@ options(continue=" ")

 @

 <<libraries>>=

-library(ff)

+##library(ff)

 library(crlmm)

 crlmm:::validCdfNames()

 if(getRversion() < "2.12.0"){

@@ -57,7 +57,7 @@ outdir <- paste("/thumper/ctsa/snpmicroarray/rs/ProcessedData/crlmm/", rpath, "/

 datadir <- "/thumper/ctsa/snpmicroarray/illumina/IDATS/370k"

 @

-Options for controlling RAM with the \Rpackage{ff} package.

+%Options for controlling RAM with the \Rpackage{ff} package.

 <<ldOptions>>=

 ldPath(outdir)

@@ -114,18 +114,41 @@ grnfiles = all(file.exists(paste(arrayNames, "_Grn.idat", sep="")))

 redfiles = all(file.exists(paste(arrayNames, "_Red.idat", sep="")))

 @

-<<samplesToProcess2>>=

+<<eval=FALSE>>=

+RG <- checkExists("RG", .path=outdir,

+		  .FUN=readIdatFiles,

+		  sampleSheet=samplesheet,

+		  path=dirname(arrayNames[1]),

+		  arrayInfoColNames=list(barcode=NULL, position="SentrixPosition"),

+		  saveDate=TRUE)

+annotation(RG) <- "human370v1c"

 crlmmResult <- checkExists("crlmmResult",

 			   .path=outdir,

-			   .FUN=crlmm:::crlmmIlluminaV2,

+			   .FUN=crlmmIllumina,

+			   RG=RG,

+			   sns=pData(RG)$ID,

+			   returnParams=TRUE,

+			   cnFile=file.path(outdir, "cnFile.rda"),

+			   snpFile=file.path(outdir, "snpFile.rda"),

+			   save.it=TRUE)

+protocolData(crlmmResult)$ScanDate <- protocolData(RG)$ScanDate

+@

+

+<<samplesToProcess2, eval=TRUE, echo=FALSE>>=

+crlmmResult <- checkExists("crlmmResult",

+			   .path=outdir,

+			   .FUN=crlmmIlluminaV2,

 			   sampleSheet=samplesheet,

 			   path=dirname(arrayNames[1]),

 			   arrayInfoColNames=list(barcode=NULL, position="SentrixPosition"),

 			   returnParams=TRUE,

 			   cnFile=file.path(outdir, "cnFile.rda"),

 			   snpFile=file.path(outdir, "snpFile.rda"),

-			   save.ab=TRUE,

+			   save.it=TRUE,

 			   cdfName="human370v1c", .load.it=FALSE)

+## MR: shouldn't this be intensities in the A element of res?

+load(file.path(outdir, "snpFile.rda"))

+res[["A"]][1:5, 1:5]

 stop()

 @

@@ -151,9 +174,10 @@ facilitating the construction of this container have been added to the

 inst/scripts directory of this package and can be sourced as follows.

 <<constructContainer2>>=

+load(file.path(outdir, "snpFile.rda"))

 batch <- as.factor(rep("1", ncol(crlmmResult)))

 container <- constructIlluminaCNSet(crlmmResult=crlmmResult, snpFile=file.path(outdir, "snpFile.rda"), cnFile=file.path(outdir, "cnFile.rda"), batch=batch)

-stop()

+A(container)[1:5, 1:5]

 @

 As described in the \texttt{copynumber} vignette, two \R{} functions

@@ -30,7 +30,9 @@ data(sample.CNSetLM)

 ## update to class CNSet

 cnSet <- as(sample.CNSetLM, "CNSet")

 all(isCurrent(cnSet)) ## is the cnSet object current?

-

+##subsetting

+cnSet2 <- cnSet[, 1:5]

+stopifnot(batchNames(cnSet2) == "C")

 \dontrun{

 	## updating class CNSetLM using ff objects

 	## a bigger object with multiple batches